Absorption of sunlight in the atmosphere of Venus

The profiles of upward, downward and net solar flux on Venus were measured at altitudes from about 62 km to the surface in three spectral bands at a vertical resolution of a few hundred meters. These data measured the penetration and absorption of solar energy in Venus' lower atmosphere quantities that are essential in evaluating the role of the greenhouse mechanism in supporting Venus' remarkably high surface temperature. In addition, the data constrained the vertical structure and optical properties of the Venus clouds

The single scattering phase functions of Jupiter's clouds

The determination of the single scattering phase functions of Jupiter's clouds and a thin upper haze by Tomasko et al. was refined and extended to seven latitudes in blue and red light. The phase function is well-constrained by the Pioneer 10 and 11 photometric data sets. Multiple scattering models were computed to match the limb darkening at each latitude at up to 15 phase angles from 12 deg to 151 deg. Ground-based observations were used for absolute calibration and to extend the data to lower phase angles. The phase functions were parameterized using the double Henyey-Greenstein function. The three Henyey-Greenstein parameters and the single scattering albedo were determined using a non-linear least squares method for the haze and the clouds below. The phase functions derived for the northen zone and belt are remarkably similar to the phase functions of the corresponding regions in the south, with most of the differences in brightness of the northern and southern features resulting from minor differences in single scattering albedo. Analysis of the Equatorial Region is complicated by the presence of numerous small features, but the phase function required is generally similar to that seen in the more homogeneous regions. Details of the phase functions of the haze and clouds are presented, and the differences between the cloud phase functions at low and high latitudes in red and blue light are discussed

Lunar maria and related deposits: Preliminary Galileo imaging results

During the Earth-Moon flyby the Galileo Solid State Imaging system obtained new information on lunar media. Imaging data in spectral bands from 0.4 to 1.0 micron wavelength provide color data for deposits on the western limb. General objectives were to determine the composition and stratigraphy of mare and related deposits for areas not previously seen well in color, and to compare the results with well-studied nearside maria. Initial results from images reduced with preliminary calibrations show that Galileo spectral reflectance data are consistent with previous earthbased observations

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is “dynamical fingerprints” which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation

The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer

Bivalent (poised or paused) chromatin comprises activating and repressing histone modifications at the same location. This combination of epigenetic marks at promoter or enhancer regions keeps genes expressed at low levels but poised for rapid activation. Typically, DNA at bivalent promoters is only lowly methylated in normal cells, but frequently shows elevated methylation levels in cancer samples. Here, we developed a universal classifier built from chromatin data that can identify cancer samples solely from hypermethylation of bivalent chromatin. Tested on over 7,000 DNA methylation data sets from several cancer types, it reaches an AUC of 0.92. Although higher levels of DNA methylation are often associated with transcriptional silencing, counter-intuitive positive statistical dependencies between DNA methylation and expression levels have been recently reported for two cancer types. Here, we re-analyze combined expression and DNA methylation data sets, comprising over 5,000 samples, and demonstrate that the conjunction of hypermethylation of bivalent chromatin and up-regulation of the corresponding genes is a general phenomenon in cancer. This up-regulation affects many developmental genes and transcription factors, including dozens of homeobox genes and other genes implicated in cancer. Thus, we reason that the disturbance of bivalent chromatin may be intimately linked to tumorigenesis

A plan for the development of superconducting Undulator prototypes for LCLS-II and future FELs

Undulators serve as the primary source of radiation for modern storage rings, and more recently for the advent of Free-Electron Lasers (FELs). The performance of future FELs can be greatly enhanced using the much higher magnetic fields of superconducting undulators (SCU) [1]. For example, the LCLS-II hard x-ray undulator can be shortened by up to 70 m using an SCU in place of a PMU (permanent magnet undulator), or its spectral performance can be critically improved when using a similar length. In addition, SCUs are expected to be orders of magnitude less sensitive to radiation dose; a major issue at LCLS-II with its 1-MHz electron bunch rate. We present a funded R&D collaboration between SLAC, ANL, and LBNL, which aims to demonstrate the viability of superconducting undulators for FELs by building, testing, measuring, and tuning two 1.5-m long planar SCU prototypes using two different technologies: NbTi at ANL and Nb Sn at LBNL. Our goal is to review and reassess the LCLS-II HXR baseline plans (PMU) in July of 2015, after the development and evaluation of both prototypes, possibly in favor of an SCU for LCLS-II.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.Additional co-authors: Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jörg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, and Manja Marz

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events